Saporin S6 is purified from the seeds of Saponaria officinalis and its CD and FT Raman spectra are determined. From the CD spectra of fresh protein aqueous and the same aqueous that was laid aside for 90 days, it is proved that saporin S6 has unusual stability. Throughout the FT Raman spectra of saporin S6, we work out that the α helix of saporin S6 is 26%, while β fold is 37%, and random coil is 37%.